Project description: Comparison between DAN and 9AA matrices using HeLa cells (HeLa control and HeLa + 2DG). For 9AA:
Date: 2022-10-23
Config: ./param_optimization/mans_opt_9AA_config.yml
Notebook version: 0.1
Optimization keys: ['Matrix']
Biological key: Treatment
Batch key: ['Matrix'] (data with different batch_keys will be processed separately)
| Unnamed: 0 | Run Order | Slide Position | Matrix | Slide Replicate | Cell Line | Treatment | datasetId | Problems | mask | Batch | generated-replicate-name | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 0 | 1 | C7 | DAN | 1 | HeLa | 2DG | 2022-10-13_15h14m23s | nan | 0 | DAN | 1-C7 |
| 1 | 1 | 2 | D2 | DAN | 1 | NIH | Control | 2022-10-13_15h17m59s | nan | 1 | DAN | 1-D2 |
| 2 | 2 | 3 | B5 | DAN | 1 | HeLa | Control | 2022-10-13_14h55m13s | nan | 0 | DAN | 1-B5 |
| 3 | 3 | 4 | B7 | DAN | 1 | HeLa | 2DG | 2022-10-13_15h06m50s | nan | 0 | DAN | 1-B7 |
| 4 | 4 | 5 | C4 | DAN | 1 | NIH | 2DG | 2022-10-13_15h08m06s | nan | 1 | DAN | 1-C4 |
| 5 | 5 | 6 | A3 | DAN | 1 | NIH | 2DG | 2022-10-13_14h43m00s | nan | 1 | DAN | 1-A3 |
| 6 | 6 | 7 | A6 | DAN | 1 | HeLa | Control | 2022-10-13_14h44m58s | nan | 0 | DAN | 1-A6 |
| 7 | 7 | 8 | D7 | DAN | 1 | HeLa | 2DG | 2022-10-13_15h22m42s | nan | 0 | DAN | 1-D7 |
| 8 | 8 | 9 | B2 | DAN | 1 | NIH | Control | 2022-10-13_14h52m47s | nan | 1 | DAN | 1-B2 |
| 9 | 9 | 10 | D3 | DAN | 1 | NIH | 2DG | 2022-10-13_15h19m13s | nan | 1 | DAN | 1-D3 |
| 10 | 10 | 11 | C6 | DAN | 1 | HeLa | Control | 2022-10-13_15h10m58s | Wrong focus | 0 | DAN | 1-C6 |
| 11 | 11 | 12 | A2 | DAN | 1 | NIH | Control | 2022-10-13_14h39m04s | Only 1/3 finished (instrument crash) | 1 | DAN | 1-A2 |
| 12 | 12 | 13 | nan | DAN | 1 | nan | Control | 2022-10-13_15h26m35s | Blank | 1 | DAN | 1-nan |
| 13 | 13 | 14 | C8 | 9AA | 2 | HeLa | 2DG | 2022-10-14_15h42m22s | nan | 0 | 9AA | 2-C8 |
| 14 | 14 | 15 | D4 | 9AA | 2 | NIH | 2DG | 2022-10-14_15h43m59s | nan | 1 | 9AA | 2-D4 |
| 15 | 15 | 16 | D8 | 9AA | 2 | HeLa | 2DG | 2022-10-14_15h49m41s | nan | 0 | 9AA | 2-D8 |
| 16 | 16 | 17 | A2 | 9AA | 2 | NIH | Control | 2022-10-14_15h32m08s | nan | 1 | 9AA | 2-A2 |
| 17 | 17 | 18 | C3 | 9AA | 2 | NIH | 2DG | 2022-10-14_15h39m03s | nan | 1 | 9AA | 2-C3 |
| 18 | 18 | 19 | A3 | 9AA | 2 | NIH | 2DG | 2022-10-14_15h33m40s | nan | 1 | 9AA | 2-A3 |
| 19 | 19 | 20 | D6 | 9AA | 2 | HeLa | Control | 2022-10-14_15h46m09s | nan | 0 | 9AA | 2-D6 |
| 20 | 20 | 21 | B6 | 9AA | 2 | HeLa | Control | 2022-10-14_15h34m36s | nan | 0 | 9AA | 2-B6 |
| 21 | 21 | 22 | C1 | 9AA | 2 | NIH | Control | 2022-10-14_15h36m37s | nan | 1 | 9AA | 2-C1 |
| 22 | 22 | 23 | D7 | 9AA | 2 | HeLa | 2DG | 2022-10-14_15h47m35s | nan | 0 | 9AA | 2-D7 |
| 23 | 23 | 24 | C6 | 9AA | 2 | HeLa | Control | 2022-10-14_15h40m19s | nan | 0 | 9AA | 2-C6 |
| 24 | 24 | 25 | C2 | 9AA | 2 | NIH | Control | 2022-10-14_15h37m31s | nan | 1 | 9AA | 2-C2 |
| 25 | 25 | 26 | A7 | DAN | 3 | HeLa | 2DG | 2022-10-14_16h01m07s | nan | 0 | DAN | 3-A7 |
| 26 | 26 | 27 | B5 | DAN | 3 | HeLa | Control | 2022-10-14_16h04m39s | nan | 0 | DAN | 3-B5 |
| 27 | 27 | 28 | C6 | DAN | 3 | HeLa | Control | 2022-10-14_16h08m17s | nan | 0 | DAN | 3-C6 |
| 28 | 28 | 29 | D8 | DAN | 3 | HeLa | 2DG | 2022-10-14_16h11m10s | nan | 0 | DAN | 3-D8 |
| 29 | 29 | 30 | A7 | 9AA | 4 | HeLa | 2DG | 2022-10-14_17h40m40s | nan | 0 | 9AA | 4-A7 |
| 30 | 30 | 31 | B5 | 9AA | 4 | HeLa | Control | 2022-10-14_17h42m08s | nan | 0 | 9AA | 4-B5 |
| 31 | 31 | 32 | nan | 9AA | 4 | nan | Control | 2022-10-14_19h28m32s | Blank | 1 | 9AA | 4-nan |
'datasetId'
When doing PCA and DE analysis, datasets belonging to the same batch are loaded together using an 'inner join': in other words, we only keep metabolites/annotations that are present in ALL datasets of a given batch. This is done to avoid artifacts in PCA analysis and volcano plots.
In general, keep in mind the following points:
| Batch | Unique pixels | Unique ions | |
|---|---|---|---|
| 0 | 9AA | 5120/5120 | 134/134 |
| 1 | DAN | 6401/6401 | 198/198 |
The size of the circles represents PCA distances (the bigger the circle, the larger the distance):
The best scenario is when both empty circles are inside the colored circle (i.e. the difference between replicates is smaller as compared to the difference between biological conditions).
To show marker intensities, all datasets are loaded again using an 'outer' join: in other words, all annotations/metabolites that appear at least in one dataset are preserved; and if a metabolite is missing in some of the datasets, its intensity will be set to zero.
| Marker name | Formula and link to plots | |
|---|---|---|
| 0 | AMP | C10H14N5O7P+Cl |
| 1 | AMP | C10H14N5O7P-H |
| 2 | Adenine | C5H5N5-H |
| 3 | Glutathione | C10H17N3O6S+Cl |
| 4 | Glutathione | C10H17N3O6S-H |
| 5 | Guanine | C5H5N5O-H |
| 6 | Uracil | C4H4N2O2-H |
| 7 | aspartate | C4H7NO4-H |
| 8 | aspartate | C4H7NO4+Cl |
| 9 | citrate | C6H8O7-H |
| 10 | fructose-bisphosphate | C6H14O12P2-H |
| 11 | fumarate | C4H4O4-H |
| 12 | fumarate | C4H4O4+Cl |
| 13 | glucose | C6H12O6-H |
| 14 | glucose | C6H12O6+Cl |
| 15 | glucose-phosphate | C6H13O9P-H |
| 16 | glutamate | C5H9NO4-H |
| 17 | glutamate | C5H9NO4+Cl |
| 18 | malate | C4H6O5+Cl |
| 19 | malate | C4H6O5-H |
| 20 | oleate | C18H34O2-H |
| 21 | palmitate | C16H32O2-H |
| 22 | succinate | C4H6O4-H |
| 23 | succinate | C4H6O4+Cl |
| 24 | taurine | C2H7NO3S+Cl |
| 25 | taurine | C2H7NO3S-H |
| 26 | threonine | C4H9NO3+Cl |
| 27 | threonine | C4H9NO3-H |
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
The following plot shows the raw intensities of intra-cellular pixels:
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets:
Detectability is defined as 'Percentage of intracellular pixels where the marker is detected with intensity above the threshold 50 (you can set this parameters in the config file).
In the following heatmap, a cross indicates that the marker was not annotated in any of the datasets (for that specific condition and choice of optimization parameters):
In the following plot, dots represent values across replicates. The number of dots can vary because the marker is not always annotated in all of the datasets: